Agriculture Reference
In-Depth Information
Most of the above work was limited by the
availability of genetic and physical maps of po-
tato that tended to be constructed from less than
ideal populations derived from segregation of as
many as four different alleles per locus from
crosses between heterozygous diploid selections.
The development of an ultradense AFLP genetic
map (van Os
et al
., 2006) was an arduous task,
which resulted in a map populated with markers
that needed subsequent conversion to PCR
markers in order to be used easily (Lo
et al
.,
2003). A potato consensus map was constructed
based on quantitative trait loci (QTLs) reported
in independent studies on potato and related
species for late blight resistance and for maturity,
since resistance to this pathogen was often asso-
ciated with maturity. QTLs were projected and
clustered into meta-QTLs for both late blight and
maturity, and used for meta-analysis to refine
genomic regions of interest. The authors sug-
gested that anchoring these meta-QTLs to the
potato genome sequence would improve candi-
date gene selection (Mueller
et al
., 2005).
However, the genomic era has given rise
to an unprecedented abundance of molecular
markers (Hamilton
et al
., 2011). In addition to
the SNPs developed from the transcriptome se-
quencing of three tetraploid cultivars that
form two tracks on the potato genome browser,
the Infinium High-Confidence SNP (69K) and
its subset, the SolCAP 8303 Infinium SNP
array, a third track comprising genome-wide
SNPs that differentiate either allele of het-
erozygous RH (a diploid hybrid of dihaploid
S. tuberosum
Group Tuberosum and
S. tubero-
sum
Group Phureja) from DM (the RH SNP
track) presents some 3.67 million SNPs identi-
fied from aligning RH illumina reads to the
PGSC v2.1.11 DM Pseudomolecules (
Fig. 17.1
).
Populations derived by crossing homozygous
DM to either of two heterozygous diploid selec-
tions were used to develop linkage maps based
on the segregation of SNP markers included
on the SolCAP 8303 Infinium Array (Felcher
et al
., 2012). The array facilitated a high-
throughput mapping scheme with wide genome
Fig.
17.
1
Screen shot of the Potato Genome Browser v4.03 showing the gene model for UDP-glucose:
solanidine glucosyltransferase (PGSC0003DMG400017508) with three single-nucleotide polymorphism
(SNP) tracks: five Infinium high-confidence SNPs, the same five SNPs that were included on the SolCAP
8303 Infinium SNP Array, and five SNPs of which only one coincided with the Infinium SNPs that were
identified from aligning the RH genome sequence against the DM reference genome. RNASeq tracks
show relative expression of the gene in six tissues, with greater expression indicated by darker shading.
